Notebook for generating mutual rank (MR) clusters
library(snowfall)
Loading required package: snowGet data
box_load(162362592785)
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|==================================================================| 100%Summarize means
save(voom.fit,fil="~/Box Sync/BrapaNetworks/voom.fit.Rdata")
Error in save(voom.fit, fil = "~/Box Sync/BrapaNetworks/voom.fit.Rdata") :
object ‘~/Box Sync/BrapaNetworks/voom.fit.Rdata’ not foundSo pretty much everything is highly significant
Start by taking the top 10000
genes.of.interest <- row.names(RIL.pvals)[1:10000]
expr.data <- voom.fit$coefficients[genes.of.interest,]
expr.data <- expr.data[,-grep("trt",colnames(expr.data))]
dim(expr.data)[1] 10000 124head(expr.data) (Intercept) pdata$RILRIL_103 pdata$RILRIL_104 pdata$RILRIL_113 pdata$RILRIL_115 pdata$RILRIL_12 pdata$RILRIL_123 pdata$RILRIL_124 pdata$RILRIL_131
Bra001964 1.082235 -4.0321896 -4.091759090 3.6994071 0.01722016 0.64266465 3.6131838 -2.8352035 3.447270788
Bra002728 5.767475 -0.5505380 -0.380674984 -3.2039164 -0.60526951 -0.81853556 -3.4589700 -3.5150262 -3.763726065
Bra002785 7.202490 -0.4198373 -0.037837754 -1.9963410 -0.04677711 -0.05993573 -2.1677690 -1.9993862 -2.291429445
Bra004960 4.733936 -3.8185006 -0.004181862 -0.2564264 0.14101788 -0.22825526 -0.6248645 -3.2303378 -3.459909583
Bra006384 4.969959 -6.8228958 -7.276735466 -0.3784078 -8.39926386 -7.41766487 -0.3806267 -0.4608661 -0.152920761
Bra006411 -2.499584 6.3062481 -0.470837158 0.1143828 -0.72175621 -1.10891611 -1.1620599 6.2134804 0.008597988
pdata$RILRIL_136 pdata$RILRIL_143 pdata$RILRIL_146 pdata$RILRIL_147 pdata$RILRIL_15 pdata$RILRIL_150 pdata$RILRIL_154 pdata$RILRIL_155 pdata$RILRIL_16
Bra001964 -2.7013520 3.9531932 -2.137003 3.8727315 -1.844875 3.82995446 -3.32072094 3.8341536 3.645469428
Bra002728 -0.8643973 -0.6859454 -3.575290 -0.7139419 -3.648528 -0.54208110 -0.54184736 -0.3414411 -0.527322860
Bra002785 0.1111586 -0.1573606 -1.996145 0.0913652 -2.072959 -0.17730162 -0.05973240 -0.1076163 -0.141110644
Bra004960 -3.1767722 -3.7877835 -3.826322 -0.1778062 -3.823915 -0.02194038 -0.06163184 -3.3049509 -0.001964347
Bra006384 -0.1949559 -0.2174621 -0.268625 -6.1696282 -6.245272 -7.54455931 -6.80442848 -6.9954140 -7.357271932
Bra006411 -0.6794655 -0.1858673 1.040992 0.1705054 6.005043 6.38883150 -0.52824769 6.4219694 6.321877192
pdata$RILRIL_164 pdata$RILRIL_166 pdata$RILRIL_171 pdata$RILRIL_174 pdata$RILRIL_175 pdata$RILRIL_176 pdata$RILRIL_182 pdata$RILRIL_183 pdata$RILRIL_184
Bra001964 3.212995 -3.52488219 -3.183956 3.9698944 3.8578812 3.6950719 -0.2901541 -4.31600771 3.8406820
Bra002728 -3.318227 -0.52510344 -3.784483 -0.4955387 -0.6376530 -0.4934072 -0.3854613 -0.39297315 -0.8917755
Bra002785 -2.296361 -0.04231166 -2.115108 -0.1911463 -0.1463134 -0.3919308 -0.4899403 -0.06608639 -0.2365228
Bra004960 -3.838495 -3.74581405 -3.349047 -3.9037685 -0.1614102 -0.2211650 -3.6020278 0.15748259 -3.1730461
Bra006384 -7.164001 -6.96733609 -7.556419 -0.2247922 -0.3388876 -6.4132492 -0.1721033 -7.90900916 -0.3785335
Bra006411 -1.840985 6.32148369 6.393611 0.5896596 -0.7447210 -0.4045582 6.1539254 -0.67620123 0.4467270
pdata$RILRIL_187 pdata$RILRIL_190 pdata$RILRIL_193 pdata$RILRIL_198 pdata$RILRIL_199 pdata$RILRIL_2 pdata$RILRIL_201 pdata$RILRIL_204 pdata$RILRIL_205
Bra001964 -4.6366460 -2.9819298 3.7899078 3.807061 3.5689148 3.7484969 -3.430264 3.779097 -3.5757733
Bra002728 -0.6933655 -3.3997308 -0.6567367 -3.259573 -0.5058403 -0.5388401 -3.375164 -3.363768 -0.5610140
Bra002785 -0.4681067 -2.0754365 -0.1426906 -2.055292 -0.3035855 -0.3874231 -2.290830 -2.164793 -0.3880579
Bra004960 -3.8036770 -3.4921676 -3.3139182 -3.473380 -0.3911074 -3.6774151 -3.708833 -3.772911 -3.4880233
Bra006384 -7.0051280 -0.1495298 -0.1448483 -6.957593 -7.9961288 -0.2478351 -6.577501 -5.906352 -5.7421265
Bra006411 6.1113273 6.0199346 -0.8270612 6.416346 6.0421259 -0.3469907 6.334644 6.159454 -0.6052733
pdata$RILRIL_206 pdata$RILRIL_207 pdata$RILRIL_208 pdata$RILRIL_21 pdata$RILRIL_211 pdata$RILRIL_212 pdata$RILRIL_213 pdata$RILRIL_215 pdata$RILRIL_222
Bra001964 3.880691 3.3828140 -0.1966156 -0.3958837 0.23450377 3.7204649 3.7298277 3.2713614 3.6393383
Bra002728 -3.761977 -0.6121855 -3.4673739 -0.2912576 -0.87593906 -0.5664787 -0.2906569 -3.3112468 -3.2993871
Bra002785 -2.056439 -0.3648677 -2.1935301 -0.4272963 -0.06998266 -0.2354231 -0.2177025 -2.1692523 -1.8157214
Bra004960 -3.408132 -3.6151195 -3.6650140 -3.4554714 -0.21103053 -3.4805881 -3.9208791 -3.7674019 -3.2889409
Bra006384 -7.350506 -6.2757201 -7.1451547 -0.1498087 -6.66569148 -7.7207016 -0.2840201 0.1454691 0.0254414
Bra006411 6.179298 6.0931093 6.3906458 6.0523161 -0.38781617 6.3215272 -1.1312831 6.1843248 6.4190943
pdata$RILRIL_223 pdata$RILRIL_225 pdata$RILRIL_228 pdata$RILRIL_229 pdata$RILRIL_23 pdata$RILRIL_232 pdata$RILRIL_234 pdata$RILRIL_235 pdata$RILRIL_240
Bra001964 3.7689147 0.1538411 3.686992 -3.57184005 -3.4189325 3.52142433 3.2289476 3.7530476 4.22611954
Bra002728 -0.8714269 -3.3875744 -3.219511 -0.55743571 -3.4591538 -3.41929785 -0.3449081 -3.3133156 -1.09828798
Bra002785 -0.1493864 -2.2130162 -1.905138 -0.31263958 -2.1685253 -1.99237889 -0.5217961 -2.4382430 0.08833911
Bra004960 -3.3154685 -3.9053096 -3.876690 -3.78409654 -0.2744527 -0.03734805 -3.8183546 -3.0557120 -0.05180437
Bra006384 -7.5136434 -7.1726709 -0.180079 -0.20023160 -6.2937009 -0.19022438 -6.2238024 -0.3653308 -7.46880852
Bra006411 6.2876465 -0.4772525 -1.230937 0.02912839 6.0872316 6.18488170 0.4420213 0.2433281 -0.88540117
pdata$RILRIL_242 pdata$RILRIL_243 pdata$RILRIL_248 pdata$RILRIL_25 pdata$RILRIL_250 pdata$RILRIL_251 pdata$RILRIL_253 pdata$RILRIL_255 pdata$RILRIL_256
Bra001964 3.408734 0.73519254 -3.3614934 -4.1080974 3.7043499 -3.39267686 -3.5972015 -4.57931560 -3.5990012
Bra002728 -3.472632 -0.69982249 -3.3818374 -0.5454432 -0.4893497 -0.37090763 -0.6239726 -0.63621999 -3.1550108
Bra002785 -2.153605 -0.06319596 -1.9777966 -0.2052215 0.2213896 -0.57254899 -0.3851680 -0.25845193 -2.1468119
Bra004960 -3.763394 -3.50815700 -0.2316513 -3.6247952 -0.2218158 0.29740732 -0.6462837 -4.06776858 -4.1103828
Bra006384 -6.669262 -6.34412452 -7.5160278 -0.3686753 -0.2707281 0.07759059 -6.7255826 0.01784094 -6.4258153
Bra006411 6.198855 6.20678883 6.2576183 6.3313488 6.3160841 6.25014985 6.1941294 6.31804278 -0.3762349
pdata$RILRIL_259 pdata$RILRIL_264 pdata$RILRIL_265 pdata$RILRIL_267 pdata$RILRIL_268 pdata$RILRIL_270 pdata$RILRIL_277 pdata$RILRIL_281 pdata$RILRIL_282
Bra001964 -4.0001493 3.8764380 0.1437703 3.9955996 3.9148454 -2.5405464 -2.71647189 -0.3022578 3.4384641
Bra002728 -3.4801726 -3.5379964 -3.6183014 -3.4930655 -3.6040317 -3.6396153 -0.59553883 -3.1909134 -0.2620543
Bra002785 -2.1490253 -2.2373581 -1.9430117 -2.1987667 -2.0095493 -2.1251230 -1.99207981 -2.0326766 -0.6052902
Bra004960 -3.8797008 -0.2170593 -0.2619773 -0.2548596 -3.4155316 0.2059798 -3.57383516 -3.5564962 -3.6712755
Bra006384 -7.4480854 -6.5916833 -0.3604226 -6.7593919 -0.2770453 -0.2857078 0.08634853 -0.3123907 -6.1821505
Bra006411 -0.5028681 6.4666495 -0.4874801 -0.6924823 6.1783602 6.6371249 0.10386305 -0.8604395 5.7877668
pdata$RILRIL_284 pdata$RILRIL_285 pdata$RILRIL_288 pdata$RILRIL_289 pdata$RILRIL_290 pdata$RILRIL_294 pdata$RILRIL_30 pdata$RILRIL_300 pdata$RILRIL_301
Bra001964 3.7006294 3.5179668 -2.1767323 3.8448285 -4.55889644 3.5994185 -2.7213018 -0.3556130 0.3120732
Bra002728 -0.2669835 -0.8425953 -0.6924283 -0.4156336 -0.30151981 -3.5207049 -3.3431448 -0.4863055 -0.5624889
Bra002785 -0.3142387 -0.3736672 -0.1161736 -0.0113959 -0.35416045 -2.1812007 -2.0830447 -0.3216474 -0.2824083
Bra004960 -3.6615439 -3.7755365 -0.1273193 -0.1199984 -3.48770351 -0.1550986 -0.2317766 -3.2720952 -0.2796088
Bra006384 -7.0895158 -7.0197303 -6.5696447 -0.1801703 -0.03079028 -7.6364646 -6.2950011 -0.1853093 -0.1331340
Bra006411 6.1290650 -0.9157409 6.2417915 -0.9812906 6.17377468 6.2746637 0.3577036 -1.1500123 0.3524955
pdata$RILRIL_303 pdata$RILRIL_308 pdata$RILRIL_31 pdata$RILRIL_311 pdata$RILRIL_318 pdata$RILRIL_325 pdata$RILRIL_329 pdata$RILRIL_332 pdata$RILRIL_337
Bra001964 3.60659393 3.6248335 -0.2696633 -2.5164443 3.49120169 -0.0680907 -3.5609622 -2.95488434 3.546517
Bra002728 -3.62822826 -0.6821739 -3.2362257 -3.4318801 -3.07089200 -3.4055799 -0.4930899 -0.63513192 -3.197417
Bra002785 -2.18520256 -0.1887345 -2.0981129 -2.4493845 -2.01990990 -2.0133385 -0.2515634 -0.15353065 -2.120596
Bra004960 -4.07093957 -3.5607205 -3.7012635 -0.4422787 -0.07833203 -3.4460046 -0.3438728 -0.05558499 -3.014790
Bra006384 0.03362311 -0.2029294 -0.2831751 -5.7990254 -0.07548398 -0.4021792 -0.2272851 -6.25523313 -7.391237
Bra006411 -0.59385762 -0.8692539 -0.9245282 0.2521411 -0.86056386 -0.1632287 -0.2450615 6.06528530 6.239817
pdata$RILRIL_339 pdata$RILRIL_340 pdata$RILRIL_341 pdata$RILRIL_344 pdata$RILRIL_346 pdata$RILRIL_347 pdata$RILRIL_353 pdata$RILRIL_354 pdata$RILRIL_355
Bra001964 -0.01162148 0.02641149 3.655514 -2.47108433 0.3616112 3.4389395 3.0214216 3.6784961 3.75633444
Bra002728 -3.57937942 -0.67258502 -3.560375 -0.49802619 -0.5634511 -3.5984131 -0.6102168 -3.5178168 -0.77955228
Bra002785 -2.16571124 -0.18212913 -2.100052 -0.07351421 -0.3152473 -1.9816915 -0.4352635 -2.0829672 -0.02174924
Bra004960 -0.23937345 -3.54458416 -3.591435 0.08902805 -4.7334046 -3.9120024 -0.2034601 -3.6213620 0.01188531
Bra006384 -6.75870986 -0.25732243 -6.714230 -7.75217634 -0.2697472 -0.1230117 -0.2271198 -6.8351148 -7.42250420
Bra006411 6.32118172 -1.07360824 6.249627 6.37490270 0.2286653 6.2025853 6.0813081 -0.4949635 -0.47606798
pdata$RILRIL_357 pdata$RILRIL_359 pdata$RILRIL_36 pdata$RILRIL_360 pdata$RILRIL_363 pdata$RILRIL_373 pdata$RILRIL_376 pdata$RILRIL_380 pdata$RILRIL_39
Bra001964 3.6950383 -4.3100033 -3.4271657 -0.1489218 -0.5445361 -3.9653698 -0.2010560 -3.6490720 3.91047287
Bra002728 -0.2527862 -3.3415918 -3.6164326 -0.4682479 -0.2100008 -0.4537577 -0.5470229 -3.4234016 -0.41019443
Bra002785 -0.2999994 -2.1157399 -2.0312578 -0.3414427 -0.2052659 -0.2916429 -0.3403611 -2.2532435 -0.06625443
Bra004960 -3.9275272 -0.2678642 -3.6541579 -3.4637913 -3.7959394 -3.2289108 -3.7681574 -4.5935767 -3.17690769
Bra006384 -7.0343445 -0.2645841 -6.2595434 -7.3149322 -7.8960576 -0.1749034 -0.1678692 -6.1225205 -6.80267807
Bra006411 6.3292925 6.2388169 -0.6247356 6.3842554 6.3180029 -1.2156699 6.0675522 -0.6898986 -0.97945774
pdata$RILRIL_42 pdata$RILRIL_46 pdata$RILRIL_53 pdata$RILRIL_60 pdata$RILRIL_63 pdata$RILRIL_65 pdata$RILRIL_66 pdata$RILRIL_69 pdata$RILRIL_7
Bra001964 -1.6696365 -2.45755109 3.8009648 3.8616843 3.688927 3.8619166 3.732366 3.76925678 -2.9895379
Bra002728 -0.6026008 -0.88788872 -3.6785906 -0.2732147 -3.639999 -0.6702721 -3.772119 -0.24172681 -3.3308452
Bra002785 -0.2135141 -0.06784988 -0.1588895 -0.2503654 -2.120015 -0.1740634 -2.090807 -0.28009513 -2.0476553
Bra004960 -0.3617700 -0.29346605 -3.2783591 -3.3238691 -3.915466 -0.2696298 -3.402791 -0.06060135 -0.1012762
Bra006384 -6.7250769 -8.03368163 -7.7442311 -0.3747482 -7.614690 -0.2746950 -7.004992 -0.41627814 -8.0957066
Bra006411 6.1997353 -0.85352764 -0.8193951 6.5327260 6.158132 -0.2632065 6.167896 6.37121259 6.3591938
pdata$RILRIL_70 pdata$RILRIL_73 pdata$RILRIL_76 pdata$RILRIL_80 pdata$RILRIL_89 pdata$RILRIL_9 pdata$RILRIL_93
Bra001964 4.0048405 3.77585306 3.7949582 -4.242327611 3.74560848 3.7594012 -2.7128624
Bra002728 -3.2976716 -3.49460179 -3.3350112 -0.519072420 -3.29589773 -0.6131951 -3.3799803
Bra002785 -1.9764443 -2.16236712 -2.3125409 -0.325579367 -2.12069734 -0.1964153 -2.2883087
Bra004960 -3.5095994 -0.03854085 -3.5955690 -0.006277264 0.02658294 -4.0556836 -0.3863463
Bra006384 -0.2067974 -6.92802940 -6.6342875 -7.688310494 -6.91719911 -7.1550888 -0.1827234
Bra006411 -0.7025772 -0.63662693 -0.9078589 6.186915132 6.28075835 6.5101318 -0.7522049expr.data[,-1] <- expr.data[,-1] + expr.data[,1] # add the intercept to the coefficients
colnames(expr.data) <- sub("pdata$RIL","",colnames(expr.data),fixed=TRUE)
head(expr.data) (Intercept) RIL_103 RIL_104 RIL_113 RIL_115 RIL_12 RIL_123 RIL_124 RIL_131 RIL_136 RIL_143 RIL_146 RIL_147 RIL_15 RIL_150
Bra001964 1.082235 -2.9499545 -3.009524 4.781642 1.099455 1.724900 4.695419 -1.752968 4.529506 -1.619117 5.0354283 -1.054767 4.954967 -0.7626394 4.912190
Bra002728 5.767475 5.2169367 5.386800 2.563558 5.162205 4.948939 2.308505 2.252449 2.003749 4.903077 5.0815293 2.192185 5.053533 2.1189468 5.225394
Bra002785 7.202490 6.7826522 7.164652 5.206149 7.155712 7.142554 5.034721 5.203103 4.911060 7.313648 7.0451290 5.206344 7.293855 5.1295302 7.025188
Bra004960 4.733936 0.9154359 4.729755 4.477510 4.874954 4.505681 4.109072 1.503599 1.274027 1.557164 0.9461529 0.907614 4.556130 0.9100218 4.711996
Bra006384 4.969959 -1.8529365 -2.306776 4.591552 -3.429305 -2.447706 4.589333 4.509093 4.817039 4.775003 4.7524972 4.701334 -1.199669 -1.2753131 -2.574600
Bra006411 -2.499584 3.8066642 -2.970421 -2.385201 -3.221340 -3.608500 -3.661644 3.713897 -2.490986 -3.179049 -2.6854511 -1.458592 -2.329079 3.5054590 3.889248
RIL_154 RIL_155 RIL_16 RIL_164 RIL_166 RIL_171 RIL_174 RIL_175 RIL_176 RIL_182 RIL_183 RIL_184 RIL_187 RIL_190 RIL_193
Bra001964 -2.238486 4.916389 4.727705 4.2952306 -2.4426470 -2.101721 5.0521295 4.940116 4.777307 0.7920811 -3.233773 4.922917 -3.5544109 -1.899695 4.872143
Bra002728 5.225627 5.426034 5.240152 2.4492478 5.2423713 1.982992 5.2719360 5.129822 5.274068 5.3820134 5.374502 4.875699 5.0741092 2.367744 5.110738
Bra002785 7.142757 7.094873 7.061379 4.9061285 7.1601779 5.087381 7.0113432 7.056176 6.810559 6.7125493 7.136403 6.965967 6.7343828 5.127053 7.059799
Bra004960 4.672305 1.428986 4.731972 0.8954409 0.9881224 1.384890 0.8301679 4.572526 4.512771 1.1319086 4.891419 1.560890 0.9302595 1.241769 1.420018
Bra006384 -1.834469 -2.025455 -2.387313 -2.1940421 -1.9973768 -2.586460 4.7451671 4.631072 -1.443290 4.7978561 -2.939050 4.591426 -2.0351687 4.820429 4.825111
Bra006411 -3.027832 3.922386 3.822293 -4.3405686 3.8218998 3.894027 -1.9099243 -3.244305 -2.904142 3.6543415 -3.175785 -2.052857 3.6117434 3.520351 -3.326645
RIL_198 RIL_199 RIL_2 RIL_201 RIL_204 RIL_205 RIL_206 RIL_207 RIL_208 RIL_21 RIL_211 RIL_212 RIL_213 RIL_215 RIL_222
Bra001964 4.889296 4.651150 4.830732 -2.348029 4.8613317 -2.4935382 4.962926 4.465049 0.8856195 0.6863515 1.316739 4.802700 4.8120629 4.3535965 4.721573
Bra002728 2.507901 5.261634 5.228635 2.392311 2.4037066 5.2064607 2.005498 5.155289 2.3001008 5.4762171 4.891536 5.200996 5.4768178 2.4562279 2.468088
Bra002785 5.147198 6.898904 6.815066 4.911660 5.0376970 6.8144317 5.146051 6.837622 5.0089595 6.7751933 7.132507 6.967066 6.9847870 5.0332373 5.386768
Bra004960 1.260557 4.342829 1.056521 1.025104 0.9610252 1.2459132 1.325804 1.118817 1.0689224 1.2784650 4.522906 1.253348 0.8130573 0.9665345 1.444996
Bra006384 -1.987634 -3.026169 4.722124 -1.607542 -0.9363929 -0.7721672 -2.380547 -1.305761 -2.1751954 4.8201506 -1.695732 -2.750742 4.6859392 5.1154284 4.995401
Bra006411 3.916762 3.542542 -2.846575 3.835061 3.6598704 -3.1048572 3.679714 3.593525 3.8910620 3.5527323 -2.887400 3.821943 -3.6308670 3.6847409 3.919510
RIL_223 RIL_225 RIL_228 RIL_229 RIL_23 RIL_232 RIL_234 RIL_235 RIL_240 RIL_242 RIL_243 RIL_248 RIL_25 RIL_250 RIL_251
Bra001964 4.851150 1.2360763 4.7692273 -2.4896049 -2.336697 4.603659 4.3111828 4.835283 5.308355 4.4909693 1.817428 -2.279258 -3.025862 4.786585 -2.310442
Bra002728 4.896048 2.3799003 2.5479633 5.2100390 2.308321 2.348177 5.4225666 2.454159 4.669187 2.2948426 5.067652 2.385637 5.222032 5.278125 5.396567
Bra002785 7.053103 4.9894733 5.2973517 6.8898500 5.033964 5.210111 6.6806935 4.764247 7.290829 5.0488844 7.139294 5.224693 6.997268 7.423879 6.629941
Bra004960 1.418468 0.8286268 0.8572469 0.9498399 4.459484 4.696588 0.9155818 1.678224 4.682132 0.9705429 1.225779 4.502285 1.109141 4.512121 5.031344
Bra006384 -2.543684 -2.2027116 4.7898803 4.7697277 -1.323742 4.779735 -1.2538431 4.604628 -2.498849 -1.6993030 -1.374165 -2.546069 4.601284 4.699231 5.047550
Bra006411 3.788063 -2.9768363 -3.7305205 -2.4704555 3.587648 3.685298 -2.0575626 -2.256256 -3.384985 3.6992716 3.707205 3.758034 3.831765 3.816500 3.750566
RIL_253 RIL_255 RIL_256 RIL_259 RIL_264 RIL_265 RIL_267 RIL_268 RIL_270 RIL_277 RIL_281 RIL_282 RIL_284 RIL_285 RIL_288
Bra001964 -2.514966 -3.4970804 -2.5167661 -2.9179142 4.958673 1.226005 5.077835 4.997081 -1.458311 -1.634237 0.7799774 4.520699 4.782865 4.6002019 -1.094497
Bra002728 5.143502 5.1312547 2.6124639 2.2873021 2.229478 2.149173 2.274409 2.163443 2.127859 5.171936 2.5765613 5.505420 5.500491 4.9248794 5.075046
Bra002785 6.817322 6.9440376 5.0556777 5.0534642 4.965131 5.259478 5.003723 5.192940 5.077367 5.210410 5.1698129 6.597199 6.888251 6.8288223 7.086316
Bra004960 4.087653 0.6661679 0.6235536 0.8542357 4.516877 4.471959 4.479077 1.318405 4.939916 1.160101 1.1774402 1.062661 1.072393 0.9583999 4.606617
Bra006384 -1.755623 4.9878002 -1.4558560 -2.4781261 -1.621724 4.609537 -1.789433 4.692914 4.684252 5.056308 4.6575686 -1.212191 -2.119557 -2.0497710 -1.599685
Bra006411 3.694545 3.8184589 -2.8758188 -3.0024520 3.967066 -2.987064 -3.192066 3.678776 4.137541 -2.395721 -3.3600233 3.288183 3.629481 -3.4153248 3.742208
RIL_289 RIL_290 RIL_294 RIL_30 RIL_300 RIL_301 RIL_303 RIL_308 RIL_31 RIL_311 RIL_318 RIL_325 RIL_329 RIL_332 RIL_337
Bra001964 4.927064 -3.476661 4.681654 -1.639067 0.7266222 1.394308 4.6888291 4.707069 0.8125718 -1.4342091 4.573437 1.014144 -2.478727 -1.872649 4.628753
Bra002728 5.351841 5.465955 2.246770 2.424330 5.2811692 5.204986 2.1392465 5.085301 2.5312490 2.3355946 2.696583 2.361895 5.274385 5.132343 2.570058
Bra002785 7.191094 6.848329 5.021289 5.119445 6.8808421 6.920081 5.0172870 7.013755 5.1043766 4.7531050 5.182580 5.189151 6.950926 7.048959 5.081894
Bra004960 4.613938 1.246233 4.578838 4.502160 1.4618412 4.454328 0.6629969 1.173216 1.0326729 4.2916577 4.655604 1.287932 4.390064 4.678351 1.719146
Bra006384 4.789789 4.939169 -2.666505 -1.325042 4.7846500 4.836825 5.0035824 4.767030 4.6867842 -0.8290661 4.894475 4.567780 4.742674 -1.285274 -2.421278
Bra006411 -3.480874 3.674191 3.775080 -2.141880 -3.6495962 -2.147088 -3.0934415 -3.368838 -3.4241121 -2.2474428 -3.360148 -2.662813 -2.744645 3.565701 3.740233
RIL_339 RIL_340 RIL_341 RIL_344 RIL_346 RIL_347 RIL_353 RIL_354 RIL_355 RIL_357 RIL_359 RIL_36 RIL_360 RIL_363 RIL_373
Bra001964 1.070614 1.108647 4.737749 -1.388849 1.4438463204 4.521175 4.103657 4.760731 4.838570 4.7772734 -3.227768 -2.344931 0.9333133 0.5376991 -2.883135
Bra002728 2.188095 5.094890 2.207100 5.269449 5.2040236047 2.169062 5.157258 2.249658 4.987922 5.5146886 2.425883 2.151042 5.2992268 5.5574739 5.313717
Bra002785 5.036778 7.020360 5.102438 7.128975 6.8872422043 5.220798 6.767226 5.119522 7.180740 6.9024902 5.086750 5.171232 6.8610468 6.9972236 6.910847
Bra004960 4.494563 1.189352 1.142502 4.822964 0.0005318176 0.821934 4.530476 1.112574 4.745822 0.8064092 4.466072 1.079779 1.2701452 0.9379970 1.505026
Bra006384 -1.788751 4.712637 -1.744271 -2.782217 4.7002120898 4.846948 4.742840 -1.865155 -2.452545 -2.0643852 4.705375 -1.289584 -2.3449728 -2.9260982 4.795056
Bra006411 3.821598 -3.573192 3.750043 3.875319 -2.2709185825 3.703001 3.581724 -2.994547 -2.975652 3.8297086 3.739233 -3.124320 3.8846715 3.8184191 -3.715254
RIL_376 RIL_380 RIL_39 RIL_42 RIL_46 RIL_53 RIL_60 RIL_63 RIL_65 RIL_66 RIL_69 RIL_7 RIL_70 RIL_73 RIL_76
Bra001964 0.8811791 -2.5668369 4.992708 -0.5874014 -1.375316 4.883200 4.943919 4.7711623 4.944152 4.814601 4.851492 -1.907303 5.087076 4.858088 4.877193
Bra002728 5.2204518 2.3440732 5.357280 5.1648739 4.879586 2.088884 5.494260 2.1274757 5.097203 1.995355 5.525748 2.436629 2.469803 2.272873 2.432464
Bra002785 6.8621284 4.9492460 7.136235 6.9889754 7.134640 7.043600 6.952124 5.0824744 7.028426 5.111683 6.922394 5.154834 5.226045 5.040122 4.889949
Bra004960 0.9657791 0.1403597 1.557029 4.3721665 4.440470 1.455577 1.410067 0.8184701 4.464307 1.331146 4.673335 4.632660 1.224337 4.695396 1.138367
Bra006384 4.8020901 -1.1525612 -1.832719 -1.7551176 -3.063722 -2.774272 4.595211 -2.6447302 4.695264 -2.035032 4.553681 -3.125747 4.763162 -1.958070 -1.664328
Bra006411 3.5679683 -3.1894824 -3.479042 3.7001514 -3.353112 -3.318979 4.033142 3.6585484 -2.762790 3.668312 3.871629 3.859610 -3.202161 -3.136211 -3.407443
RIL_80 RIL_89 RIL_9 RIL_93
Bra001964 -3.160092 4.827844 4.8416364 -1.630627
Bra002728 5.248402 2.471577 5.1542796 2.387494
Bra002785 6.876910 5.081792 7.0060742 4.914181
Bra004960 4.727659 4.760519 0.6782528 4.347590
Bra006384 -2.718351 -1.947240 -2.1851295 4.787236
Bra006411 3.687331 3.781174 4.0105479 -3.251789Get Rob’s Data
blups2011 <- box_read_csv(164446516413)Remote file '/var/folders/xr/9cbydt955pj42zfq6mc_y5g40000gn/T//RtmpYRCgLR/Brapa2011BayesHeight_blups.csv' read into memory as an object of class data.frameblups2012 <- box_read_csv(164446639332)Remote file '/var/folders/xr/9cbydt955pj42zfq6mc_y5g40000gn/T//RtmpYRCgLR/Brapa2012BayesHeight_blups.csv' read into memory as an object of class data.frameblups2011$Line %<>% paste("RIL",.,sep="_")
blups2012$Line %<>% paste("RIL",.,sep="_")
head(blups2011)head(blups2012)Merge Data
blups.combined <- merge(blups2011,blups2012,by="Line",all=TRUE, suffixes=c(".2011",".2012"))
blups.combined %<>% subset(select=!grepl("V1|individual|blk|trt|treat",colnames(.)))
head(blups.combined)expr.blup <- merge(blups.combined,t(expr.data),by.x="Line",by.y=0)
head(expr.blup)Correlation
expr.blup.cor <- cor(expr.blup[,-1])Mutual Rank
sfInit(parallel = TRUE, cpus=4)snowfall 1.84-6.1 initialized (using snow 0.4-2): parallel execution on 4 CPUs.expr.blup.rank <- sfApply(expr.blup.cor,2,function(x) rank(-abs(x)))
expr.blup.rank[1:10,1:10] UNr.2011 UNHmax.2011 UNInflect_DD UNInflect_size UNduration.2011 UNSTP.2011 UNr.2012 CRr UNHmax.2012 CRHmax
UNr.2011 1 7599.0 2510 7599.0 18 7255 262 2200 4879.0 6045
UNHmax.2011 5293 1.5 9 1.5 19 2 3732 933 8.0 11
UNInflect_DD 649 329.0 1 329.0 2 349 3684 1647 596.0 713
UNInflect_size 5292 1.5 8 1.5 20 3 3733 934 7.0 10
UNduration.2011 2 614.0 2 614.0 1 617 689 524 1353.0 1558
UNSTP.2011 4719 3.0 11 3.0 15 1 3634 908 9.0 9
UNr.2012 8 5166.0 3772 5166.0 540 5098 1 2 3841.0 3352
CRr 152 1441.0 836 1441.0 81 1451 2 1 939.0 811
UNHmax.2012 785 6.0 13 6.0 62 6 1647 168 1.5 5
CRHmax 1856 8.0 15 8.0 66 8 1011 62 6.0 1expr.blup.mr <- sqrt(expr.blup.rank*t(expr.blup.rank))
expr.blup.mr[1:10,1:10] UNr.2011 UNHmax.2011 UNInflect_DD UNInflect_size UNduration.2011 UNSTP.2011 UNr.2012 CRr UNHmax.2012 CRHmax
UNr.2011 1.00000 6342.042810 1276.31893 6341.443684 6.00000 5851.183214 45.78209 578.2733 1957.042411 3349.555194
UNHmax.2011 6342.04281 1.500000 54.41507 1.500000 108.00926 2.449490 4390.84411 1159.5055 6.928203 9.380832
UNInflect_DD 1276.31893 54.415071 1.00000 51.303021 2.00000 61.959664 3727.74033 1173.4104 88.022724 103.416633
UNInflect_size 6341.44368 1.500000 51.30302 1.500000 110.81516 3.000000 4391.43234 1160.1267 6.480741 8.944272
UNduration.2011 6.00000 108.009259 2.00000 110.815161 1.00000 96.202911 609.96721 206.0194 289.630799 320.668053
UNSTP.2011 5851.18321 2.449490 61.95966 3.000000 96.20291 1.000000 4304.19934 1147.8275 7.348469 8.485281
UNr.2012 45.78209 4390.844110 3727.74033 4391.432340 609.96721 4304.199345 1.00000 2.0000 2515.179318 1840.888916
CRr 578.27329 1159.505498 1173.41041 1160.126717 206.01942 1147.827513 2.00000 1.0000 397.180060 224.236482
UNHmax.2012 1957.04241 6.928203 88.02272 6.480741 289.63080 7.348469 2515.17932 397.1801 1.500000 5.477226
CRHmax 3349.55519 9.380832 103.41663 8.944272 320.66805 8.485281 1840.88892 224.2365 5.477226 1.000000sfStop()
Stopping clustersave.image(file = "~/Box Sync/BrapaNetworks/MR.Rdata")Get graphs at different MR
First: define some functions
Use different MR thresholds of 10 to 210 (absolute values) to build the network (genes with a correlation higher than the threshold were considered connected). I then subset the network to take all genes “directly” connected to LFY.
null device
1